tonights.parameters['dir'] = os.getcwd()+'/'+tonights.parameters['trunk']
subprocess.call(["mkdir","-p",tonights.parameters['dir']])
# ------------------------------------------------------------------
# Pickle the bureau, sample, and database, if required. If we do
# this, its because we want to pick up from where we left off
# (ie with SWAPSHOP) - so save the pickles in the $cwd. This is
# taken care of in io.py. Note that we update the parameters as
# we go - this will be useful later when we write update.config.
if tonights.parameters['repickle'] and count > 0:
new_bureaufile = swap.get_new_filename(tonights.parameters,'bureau')
print "SWAP: saving agents to "+new_bureaufile
swap.write_pickle(bureau,new_bureaufile)
tonights.parameters['bureaufile'] = new_bureaufile
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "SWAP: saving subjects to "+new_samplefile
swap.write_pickle(sample,new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
if practise:
new_dbfile = swap.get_new_filename(tonights.parameters,'database')
print "SWAP: saving database to "+new_dbfile
swap.write_pickle(db,new_dbfile)
tonights.parameters['dbfile'] = new_dbfile
# ------------------------------------------------------------------
tonights.parameters['dir'] = os.getcwd(
) + '/' + tonights.parameters['trunk']
subprocess.call(["mkdir", "-p", tonights.parameters['dir']])
# ------------------------------------------------------------------
# Pickle the bureau, sample, and database, if required. If we do
# this, its because we want to pick up from where we left off
# (ie with SWAPSHOP) - so save the pickles in the $cwd. This is
# taken care of in io.py. Note that we update the parameters as
# we go - this will be useful later when we write update.config.
if tonights.parameters['repickle'] and count > 0:
new_bureaufile = swap.get_new_filename(tonights.parameters, 'bureau')
print "SWAP: saving agents to " + new_bureaufile
swap.write_pickle(bureau, new_bureaufile)
tonights.parameters['bureaufile'] = new_bureaufile
new_samplefile = swap.get_new_filename(tonights.parameters,
'collection')
print "SWAP: saving subjects to " + new_samplefile
swap.write_pickle(sample, new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
if practise:
new_dbfile = swap.get_new_filename(tonights.parameters, 'database')
print "SWAP: saving database to " + new_dbfile
swap.write_pickle(db, new_dbfile)
tonights.parameters['dbfile'] = new_dbfile
# ------------------------------------------------------------------
def make_offline_reports(args):
"""
NAME
make_offline_reports
PURPOSE
Given an offline tuple as well as other bureau tuples etc,
this script produces the reports made at the end of SWAP
COMMENTS
FLAGS
-h Print this message
--out Output directory, otherwise is '.'
--do_offline Do offline analysis?
INPUTS
configfile Plain text file containing SW experiment configuration
bureaufile
collectionfile
OUTPUTS
EXAMPLE
BUGS
AUTHORS
This file is part of the Space Warps project, and is distributed
under the MIT license by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2014-09-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
# default settings are for offline using only exact training info
flags = {'do_offline': False,
'output_directory': '.',
'PL0': 0.5, # initial PL guess
'PD0': 0.5, # initial PD guess
'pi': 4e-2, # initial lens probability
'n_min_assessment': 0, # minimum number of assessments before included in analysis
'use_training_info': True,
'exclude_test_info': True,
'exclude_training_info': False,
'N_min': 10, # min number of EM steps required
'N_max': 100, # max number of EM steps
'epsilon_min': 1e-6, # escape condition
}
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'config':
configfile = args[arg]
elif arg == 'collection':
collectionfile = args[arg]
elif arg == 'bureau':
bureaufile = args[arg]
else:
print "make_offline_reports: unrecognized flag ",arg
out_dir = flags['output_directory']
# ------------------------------------------------------------------
# Read in run configuration:
tonights = swap.Configuration(configfile)
# TODO: do this correctly
tonights.parameters['finish'] = 'now'
tonights.parameters['start'] = 'now'
tonights.parameters['trunk'] = \
tonights.parameters['survey']+'_'+tonights.parameters['finish']
tonights.parameters['dir'] = out_dir
# How will we make decisions based on probability?
thresholds = {}
thresholds['detection'] = tonights.parameters['detection_threshold']
thresholds['rejection'] = tonights.parameters['rejection_threshold']
t = -1 # for now?!
# ------------------------------------------------------------------
# Read in, or create, a bureau of agents who will represent the
# volunteers:
bureau = swap.read_pickle(bureaufile, 'bureau')
# ------------------------------------------------------------------
# Read in, or create, an object representing the candidate list:
sample = swap.read_pickle(collectionfile, 'collection')
# ------------------------------------------------------------------
# if do_offline, run offline analysis here:
if flags['do_offline']:
PL0 = flags['PL0']
PD0 = flags['PD0']
pi = flags['pi']
n_min_assessment = flags['n_min_assessment']
use_training_info = flags['use_training_info']
exclude_test_info = flags['exclude_test_info']
exclude_training_info = flags['exclude_training_info']
N_min = flags['N_min']
N_max = flags['N_max']
epsilon_min = flags['epsilon_min']
# initialize offline params
bureau_offline = {}
probabilities = {}
online_probabilities = {}
training_IDs = {} # which entries in collection are training
set_aside_subject = {} # which subjects do we set aside? Here we set aside none
set_aside_agent = {} # which agents do we set aside? Here we set aside none
collection = {}
for ID in sample.list():
if ID in set_aside_subject:
continue
else:
collection.update({ID: sample.member[ID]})
for ID in collection.keys():
subject = collection[ID]
n_assessment = len(subject.annotationhistory['ItWas'])
if (n_assessment > n_min_assessment):
if (subject.category == 'training'):
if use_training_info:
truth = {'LENS': 1, 'NOT': 0}[subject.truth]
training_IDs.update({ID: truth})
if exclude_training_info:
# when doing M step, don't use these to update parameters
training_IDs.update({ID: -1})
elif (subject.category == 'test'):
if exclude_test_info:
# when doing M step, don't use these to update parameters
training_IDs.update({ID: -1})
probabilities.update({ID: pi})
online_probabilities.update({ID: subject.mean_probability})
for agent_i in xrange(len(subject.annotationhistory['Name'])):
name = subject.annotationhistory['Name'][agent_i]
if name in set_aside_agent:
continue
xij = subject.annotationhistory['ItWas'][agent_i]
if name not in bureau_offline:
bureau_offline.update({name: {
'PD': PD0, 'PL': PL0,
'PL_in': bureau.member[name].PL,
'PD_in': bureau.member[name].PD,
'Pi': pi,
'Subjects': {ID: xij}}})
else:
bureau_offline[name]['Subjects'].update({ID: xij})
# Run EM Algorithm
bureau_offline, pi, probabilities, information_dict = EM_algorithm(
bureau_offline, pi, probabilities, training_IDs,
N_min=N_min, N_max=N_max, epsilon_min=epsilon_min,
return_information=True)
tup = (bureau_offline, pi, probabilities, information_dict)
offlinefile = out_dir + '/offline.pickle'
swap.write_pickle(tup, offlinefile)
# ------------------------------------------------------------------
# Now replace sample member probabilities with offline probabilities
# Also update bureau with offline results
for ID in sample.list():
# just in case any IDs didn't get into offline somehow?!
if ID not in probabilities.keys():
sample.member.pop(ID)
continue
# This is a bit hackish: update mean_probability,
# median_probability, and do the rejection threshold stuff
subject = sample.member[ID]
subject.mean_probability = probabilities[ID]
subject.median_probability = probabilities[ID]
# ripped from subject.py
if subject.mean_probability < subject.rejection_threshold:
subject.status = 'rejected'
if subject.kind == 'test':
subject.state = 'inactive'
subject.retirement_time = -1#at_time
subject.retirement_age = subject.exposure
elif subject.mean_probability > subject.detection_threshold:
subject.status = 'detected'
if subject.kind == 'test':
# Let's keep the detections live!
# subject.state = 'inactive'
# subject.retirement_time = at_time
# subject.retirement_age = subject.exposure
pass
else:
# Keep the subject alive! This code is only reached if
# we are not being hasty.
subject.status = 'undecided'
if subject.kind == 'test':
subject.state = 'active'
subject.retirement_time = 'not yet'
subject.retirement_age = 0.0
# I don't think this is necessary, but just in case
sample.member[ID] = subject
for kind in ['sim', 'dud', 'test']:
sample.collect_probabilities(kind)
# now save
collectionfile = out_dir + '/collection_offline.pickle'
swap.write_pickle(collection, collectionfile)
# now update bureau
for ID in bureau.list():
# just in case any IDs didn't make it to offline?
if ID not in bureau_offline.keys():
bureau.member.pop(ID)
continue
# update PL, PD, then update_skill
agent = bureau.member[ID]
agent.PL = bureau_offline[ID]['PL']
agent.PD = bureau_offline[ID]['PD']
agent.update_skill()
# I don't think this is necessary, but just in case
bureau.member[ID] = agent
bureau.collect_probabilities()
# now save
bureaufile = out_dir + '/bureau_offline.pickle'
swap.write_pickle(bureau, bureaufile)
# ------------------------------------------------------------------
# now we can pretend we're in SWAP.py
new_retirementfile = swap.get_new_filename(tonights.parameters,'retire_these')
print "make_offline_reports: saving retiree subject Zooniverse IDs..."
N = swap.write_list(sample,new_retirementfile,item='retired_subject')
print "make_offline_reports: "+str(N)+" lines written to "+new_retirementfile
# Also print out lists of detections etc! These are urls of images.
new_samplefile = swap.get_new_filename(tonights.parameters,'candidates')
print "make_offline_reports: saving lens candidates..."
N = swap.write_list(sample,new_samplefile,item='candidate')
print "make_offline_reports: "+str(N)+" lines written to "+new_samplefile
# Now save the training images, for inspection:
new_samplefile = swap.get_new_filename(tonights.parameters,'training_true_positives')
print "make_offline_reports: saving true positives..."
N = swap.write_list(sample,new_samplefile,item='true_positive')
print "make_offline_reports: "+str(N)+" lines written to "+new_samplefile
new_samplefile = swap.get_new_filename(tonights.parameters,'training_false_positives')
print "make_offline_reports: saving false positives..."
N = swap.write_list(sample,new_samplefile,item='false_positive')
print "make_offline_reports: "+str(N)+" lines written to "+new_samplefile
new_samplefile = swap.get_new_filename(tonights.parameters,'training_false_negatives')
print "make_offline_reports: saving false negatives..."
N = swap.write_list(sample,new_samplefile,item='false_negative')
print "make_offline_reports: "+str(N)+" lines written to "+new_samplefile
# Also write out catalogs of subjects, including the ZooID, subject ID,
# how many classifications, and probability:
catalog = swap.get_new_filename(tonights.parameters,'candidate_catalog')
print "make_offline_reports: saving catalog of high probability subjects..."
Nlenses,Nsubjects = swap.write_catalog(sample,catalog,thresholds,kind='test')
print "make_offline_reports: From "+str(Nsubjects)+" subjects classified,"
print "make_offline_reports: "+str(Nlenses)+" candidates (with P > rejection) written to "+catalog
catalog = swap.get_new_filename(tonights.parameters,'sim_catalog')
print "make_offline_reports: saving catalog of high probability subjects..."
Nsims,Nsubjects = swap.write_catalog(sample,catalog,thresholds,kind='sim')
print "make_offline_reports: From "+str(Nsubjects)+" subjects classified,"
print "make_offline_reports: "+str(Nsims)+" sim 'candidates' (with P > rejection) written to "+catalog
catalog = swap.get_new_filename(tonights.parameters,'dud_catalog')
print "make_offline_reports: saving catalog of high probability subjects..."
Nduds,Nsubjects = swap.write_catalog(sample,catalog,thresholds,kind='dud')
print "make_offline_reports: From "+str(Nsubjects)+" subjects classified,"
print "make_offline_reports: "+str(Nduds)+" dud 'candidates' (with P > rejection) written to "+catalog
# ------------------------------------------------------------------
# Make plots! Can't plot everything - uniformly sample 200 of each
# thing (agent or subject).
# Agent histories:
fig1 = bureau.start_history_plot()
pngfile = swap.get_new_filename(tonights.parameters,'histories')
Nc = np.min([200,bureau.size()])
print "make_offline_reports: plotting "+str(Nc)+" agent histories in "+pngfile
for Name in bureau.shortlist(Nc):
bureau.member[Name].plot_history(fig1)
bureau.finish_history_plot(fig1,t,pngfile)
tonights.parameters['historiesplot'] = pngfile
# Agent probabilities:
pngfile = swap.get_new_filename(tonights.parameters,'probabilities')
print "make_offline_reports: plotting "+str(Nc)+" agent probabilities in "+pngfile
bureau.plot_probabilities(Nc,t,pngfile)
tonights.parameters['probabilitiesplot'] = pngfile
# Subject trajectories:
fig3 = sample.start_trajectory_plot()
pngfile = swap.get_new_filename(tonights.parameters,'trajectories')
# Random 500 for display purposes:
Ns = np.min([500,sample.size()])
print "make_offline_reports: plotting "+str(Ns)+" subject trajectories in "+pngfile
for ID in sample.shortlist(Ns):
sample.member[ID].plot_trajectory(fig3)
# To plot only false negatives, or only true positives:
# for ID in sample.shortlist(Ns,kind='sim',status='rejected'):
# sample.member[ID].plot_trajectory(fig3)
# for ID in sample.shortlist(Ns,kind='sim',status='detected'):
# sample.member[ID].plot_trajectory(fig3)
sample.finish_trajectory_plot(fig3,pngfile,t=t)
tonights.parameters['trajectoriesplot'] = pngfile
# Candidates! Plot all undecideds or detections:
fig4 = sample.start_trajectory_plot(final=True)
pngfile = swap.get_new_filename(tonights.parameters,'sample')
# BigN = 100000 # Would get them all...
BigN = 500 # Can't see them all!
candidates = []
candidates += sample.shortlist(BigN,kind='test',status='detected')
candidates += sample.shortlist(BigN,kind='test',status='undecided')
sims = []
sims += sample.shortlist(BigN,kind='sim',status='detected')
sims += sample.shortlist(BigN,kind='sim',status='undecided')
duds = []
duds += sample.shortlist(BigN,kind='dud',status='detected')
duds += sample.shortlist(BigN,kind='dud',status='undecided')
print "make_offline_reports: plotting "+str(len(sims))+" sims in "+pngfile
for ID in sims:
sample.member[ID].plot_trajectory(fig4)
print "make_offline_reports: plotting "+str(len(duds))+" duds in "+pngfile
for ID in duds:
sample.member[ID].plot_trajectory(fig4)
print "make_offline_reports: plotting "+str(len(candidates))+" candidates in "+pngfile
for ID in candidates:
sample.member[ID].plot_trajectory(fig4)
# They will all show up in the histogram though:
sample.finish_trajectory_plot(fig4,pngfile,final=True)
tonights.parameters['candidatesplot'] = pngfile
# ------------------------------------------------------------------
# Finally, write a PDF report:
swap.write_report(tonights.parameters,bureau,sample)
equal = N1+N2==N3
print "SWAP: SANITY CHECK! %i + %i = %i? %s"%(N1,N2,N3, equal)
# ------------------------------------------------------------------
# Pickle the bureau, sample, and database, if required. If we do
# this, its because we want to pick up from where we left off
# (ie with SWAPSHOP) - so save the pickles in the $cwd. This is
# taken care of in io.py. Note that we update the parameters as
# we go - this will be useful later when we write update.config.
if tonights.parameters['repickle'] and count > 0:
new_bureaufile = swap.get_new_filename(tonights.parameters,'bureau')
print "SWAP: saving agents to "+new_bureaufile
swap.write_pickle(bureau,new_bureaufile)
tonights.parameters['bureaufile'] = new_bureaufile
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "SWAP: saving subjects to "+new_samplefile
swap.write_pickle(sample,new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "SWAP: saving metadata to "+metadatafile
swap.write_pickle(storage,metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# ------------------------------------------------------------------
# If there is more to do we need to update the config file for the next day
def make_lens_catalog(args):
"""
NAME
make_lens_catalog
PURPOSE
Given location of collection pickle, this script produces a set of
annotated images of lenses (heatmaps for lens locations, markers for
where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--skill Weight by skill
INPUTS
collection.pickle
OUTPUTS
lens.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
EXAMPLE
BUGS
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {'skill': False,
'output_directory': './',
'output_name': 'catalog.dat',
'image_y_size': 440,
'catalog_path': '',
'update_collection': '',}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection_path':
collection_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ",arg
print "make_lens_catalog: illustrating behaviour captured in collection file: "
print "make_lens_catalog: ",collection_path
memory = joblib.Memory(cachedir=flags['output_directory'])
memory.clear()
catalog_path = flags['output_directory'] + flags['output_name']
if len(flags['output_name']) > 0:
F = open(catalog_path, 'w')
F.write('id,kind,x,y,prob,n0,skill,dist\n')
# ------------------------------------------------------------------
# Read in files:
collection = swap.read_pickle(collection_path, 'collection')
ID_list = collection.list()
print "make_lens_catalog: collection numbers ", len(ID_list)
if flags['catalog_path'] != '':
print "make_lens_catalog: filtering from catalog ",flags['catalog_path']
catalog_in = csv2rec(flags['catalog_path'])
ID_list = np.unique(catalog_in['id'])
# ------------------------------------------------------------------
# Run through data:
catalog = {}
for ID in ID_list:
subject = collection.member[ID]
kind = subject.kind
P = subject.mean_probability
itwas = subject.annotationhistory['ItWas']
x_all = subject.annotationhistory['At_X']
y_all = subject.annotationhistory['At_Y']
x_markers = np.array([xi for xj in x_all for xi in xj])
y_markers = np.array([yi for yj in y_all for yi in yj])
catalog.update({ID: {'agents_reject': [],
'x': x_markers,
'y': y_markers,}})
PL_all = subject.annotationhistory['PL']
PD_all = subject.annotationhistory['PD']
# filter out the empty clicks
PL_list = []
PL_nots = []
for i, xj in enumerate(x_all):
# len(xj) of empty = 0
PL_list.append([PL_all[i]] * len(xj))
if len(xj) == 0:
PL_nots.append(PL_all[i])
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
PL_nots = np.array(PL_nots)
# filter out the empty clicks
PD_list = []
PD_nots = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
if len(xj) == 0:
PD_nots.append(PD_all[i])
catalog[ID]['agents_reject'].append(i)
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
PD_nots = np.array(PD_nots)
skill = swap.expectedInformationGain(0.5, PL, PD) # skill
# it is only fair to write out the NOTs, too
# do the empty guys
skill_nots = swap.expectedInformationGain(0.5, PL_nots, PD_nots) # skill
x, y = -1, -1
N0 = len(skill_nots)
S = np.sum(skill_nots)
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
if len(catalog)%500 == 0:
print len(catalog)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
if len(x_markers) == 0:
# apparently everyone was a not...
catalog[ID]['agents_labels'] = np.array([])
continue
# ------------------------------------------------------------------
# cluster
print 'make_lens_catalog: subject ID = ', ID
if flags['skill']:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, skill, memory=memory)
else:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, None, memory=memory)
# need to get: x, y, N0, S
catalog[ID]['agents_labels'] = cluster_labels
for cluster_center_label in cluster_center_labels:
cluster_center = cluster_centers[cluster_center_label]
members = (cluster_labels == cluster_center_label)
x, y = cluster_center
# convert y to catalog convention
y = flags['image_y_size'] - y
N0 = np.sum(members)
S = np.sum(skill[members])
D = dist_within[cluster_center_label]
if cluster_center_label == -1:
# outlier cluster
# so really every point is its own cluster...
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
## if len(catalog)%500 == 0:
## print len(catalog)
# TODO: make some requirement to be included (exclude outliers)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
print 'make_lens_catalog: Clearing memory'
# clear memory
memory.clear()
if len(flags['output_name']) > 0:
print 'make_lens_catalog: closing file!'
F.close()
if len(flags['update_collection']) > 0:
print 'make_lens_catalog: writing updated collection to', flags['update_collection']
# TODO: get the other params correct!!!!
collection_fat = swap.collection.Collection()
for ID in catalog:
subject = collection.member[ID]
atx = subject.annotationhistory['At_X']
labels_in = list(catalog[ID]['agents_labels'])
labels_fat = []
for atx_i in atx:
labels_fat.append([])
for atx_ij in atx_i:
labels_fat[-1].append(labels_in.pop(0))
subject.annotationhistory.update({'labels': labels_fat})
collection_fat.member.update({ID: subject})
swap.write_pickle(collection_fat, flags['update_collection'])
print 'make_lens_catalog: All done!'
return catalog
def MachineShop(args):
# Buh. I never built in the ability to change directories on the fly
#machine_sim_directory = 'sims_Machine/redo_with_circular_morphs'
"""
Sometimes you just need to the run the Machine on a bunch of already
made SWAP-runs / simulations.
If so, this script is for you!
"""
# Get parameters from the SWAP run of interest
the = swap.Configuration(args.config)
params = the.parameters
# This pulls up the FIDUCIAL SWAP simulation
sim = Simulation(config=args.config,
directory='sims_SWAP/S_PLPD5_p5_ff_norand',
variety='feat_or_not')
# this was originally set to 2/17/09 which is WRONG
# 11/2/17: WHY?? F**k you, Past Melanie. What am I supposed to do here??
first_day = dt.datetime(2009, 2, 12)
today = dt.datetime.strptime(params['start'], '%Y-%m-%d_%H:%M:%S')
start_day = dt.datetime(2009, 2, 17)
last_day = dt.datetime.strptime(params['end'], '%Y-%m-%d_%H:%M:%S')
yesterday = None
run_machine = False
SWAP_retired = 0
notfound = 0
last_night = None
for idx, filename in enumerate(sim.retiredFileList[(today -
first_day).days:]):
print ""
print "----------------------- The Machine Shop ----------------------------"
print "Today is {}".format(today)
if today >= last_day:
print "Get outta the machine shop!"
exit()
# ---------------------------------------------------------------------
# OPEN METADATA PICKLE (updated each time MachineClassifier is run)
# ---------------------------------------------------------------------
backup_meta_file = params['metadatafile'].replace(
'.pickle', '_orig.pickle')
if today == first_day:
try:
storage = swap.read_pickle(backup_meta_file, 'metadata')
except:
print "MachineShop: Backup metadata pickle not yet created."
print "MachineShop: Opening original metadata pickle file instead"
storage = swap.read_pickle(params['metadatafile'], 'metadata')
if 'retired_date' not in storage.subjects.colnames:
storage.subjects['retired_date'] = '2016-09-10'
if 'valid' not in np.unique(storage.subjects['MLsample']):
expert = (storage.subjects['Expert_label'] != -1)
storage.subjects['MLsample'][expert] = 'valid'
# save an untouched copy for reference later
print "MachineShop: Creating a backup metadata pickle"
swap.write_pickle(storage, backup_meta_file)
else:
storage = swap.read_pickle(params['metadatafile'], 'metadata')
# Regardless of which metadata you open, make sure it has these columns
# (old metadata files WON'T have them!)
if 'retired_date' not in storage.subjects.colnames:
storage.subjects['retired_date'] = '2016-09-10'
if 'valid' not in np.unique(storage.subjects['MLsample']):
expert = (storage.subjects['Expert_label'] != -1)
storage.subjects['MLsample'][expert] = 'valid'
subjects = storage.subjects
# I just need to know what was retired TONIGHT --
# compare what's retired UP TILL tonight with what was
# retired up till LAST NIGHT
SWAP_retired_by_tonight = sim.fetchCatalog(filename)
# If we're picking up where we left off, grab previous training sample
#if today>start_day and last_night is None:
# print 'MachineShop: getting previous training sample'
# last_night = subjects[subjects['MLsample']=='train']
# last_night['zooid'] = last_night['SDSS_id']
try:
ids_retired_tonight = set(SWAP_retired_by_tonight['zooid']) - \
set(last_night['zooid'])
except:
ids_retired_tonight = set(SWAP_retired_by_tonight['zooid'])
print "Newly retired subjects: {}".format(len(ids_retired_tonight))
# Now that I have the ids from the previous night, adjust the
# metadata file to reflect what was retired / add SWAP info
for ID in list(ids_retired_tonight):
# Locate this subject in the metadata file
mask = subjects['SDSS_id'] == int(ID)
# Update them in metadata file as training sample for MC
# DOUBLE CHECK THAT IT HAS NOT BEEN RETIRED BY MACHINE!!!
#if subjects['MLsample'][mask] == 'test ':
if subjects['MLsample'][mask] == 'test':
SWAP_retired += 1
subjects['MLsample'][mask] = 'train'
subjects['retired_date'][mask] = dt.datetime.strftime(
today, '%Y-%m-%d')
subjects['SWAP_prob'][mask] = SWAP_retired_by_tonight['P'][
SWAP_retired_by_tonight['zooid'] == ID]
run_machine = True
else:
notfound += 1
if len(subjects[subjects['MLsample'] == 'train']) >= 10000:
run_machine = True
last_night = SWAP_retired_by_tonight
print "Retired by this day:", len(last_night)
print ""
print "MachineShop: Found {0} subjects retired by SWAP on {1}"\
.format(SWAP_retired, today)
print "MachineShop: {0} total subjects retired so far"\
.format(np.sum(subjects['MLsample']=='train'))
print "MachineShop: Found {0} subjects retired by Machine."\
.format(np.sum(subjects['MLsample']=='mclas'))
print "MachineShop: Saving updated StorageLocker."
params['dir'] = os.getcwd()
# Save our new metadata file -- MC needs this -- save to NOT the original
params['metadatafile'] = params['dir'] + '/' + params[
'survey'] + '_metadata.pickle'
swap.write_pickle(storage, params['metadatafile'])
if run_machine:
# Need to doctor the config to refect the "correct date"
params['start'] = today.strftime('%Y-%m-%d_%H:%M:%S')
swap.write_config(args.config, params)
# Run MachineClassifier.py using this subject file
os.system("python MachineClassifier.py -c %s" % args.config)
"""os.system("python test_Machine.py -c {0}".format(args.config))"""
# MachineClassifier updates the configfile so now we need to open the NEW one
the = swap.Configuration(args.config)
params = the.parameters
# Update date (since we're not running SWAP)
today += dt.timedelta(days=1)
def MachineClassifier(options, args):
try: config = options.configfile
except: pdb.set_trace()
tonights = swap.Configuration(config)
#"""
# Read the pickled random state file
random_file = open(tonights.parameters['random_file'],"r");
random_state = cPickle.load(random_file);
random_file.close();
np.random.set_state(random_state);
#"""
# Get the machine threshold (make retirement decisions)
threshold = tonights.parameters['machine_threshold']
# Get list of evaluation metrics and criteria
eval_metrics = tonights.parameters['evaluation_metrics']
survey = tonights.parameters['survey']
subdir = 'sup_run4'
#----------------------------------------------------------------------
# read in the metadata for all subjects (Test or Training sample?)
subjects = swap.read_pickle(tonights.parameters['metadatafile'], 'metadata')
#----------------------------------------------------------------------
# read in the SWAP collection
sample = swap.read_pickle(tonights.parameters['samplefile'],'collection')
#----------------------------------------------------------------------
# read in or create the ML collection
MLsample = swap.read_pickle(tonights.parameters['MLsamplefile'],
'MLcollection')
# read in or create the ML bureau for machine agents (history)
MLbureau = swap.read_pickle(tonights.parameters['MLbureaufile'], 'MLbureau')
#-----------------------------------------------------------------------
# DETERMINE IF THERE IS A TRAINING SAMPLE TO WORK WITH
#-----------------------------------------------------------------------
# TO DO: training sample should only select those which are NOT part of
# validation sample (Nair catalog objects) 2/22/16
# IDENTIFY TRAINING SAMPLE
train_sample = subjects[subjects['MLsample']=='train']
train_meta, train_features = ml.extract_training(train_sample)
train_labels = np.array([1 if p > 0.3 else 0 \
for p in train_meta['SWAP_prob']])
# IDENTIFY VALIDATION SAMPLE (FINAL)
valid_sample = subjects[subjects['MLsample']=='valid']
valid_meta, valid_features = ml.extract_training(valid_sample)
valid_labels = valid_meta['Expert_label'].filled()
#if len(train_sample) >= 100:
# TO DO: LOOP THROUGH DIFFERENT MACHINES? HOW MANY MACHINES?
for metric in eval_metrics:
# REGISTER Machine Classifier
# Construct machine name --> Machine+Metric? For now: KNC
machine = 'KNC'
Name = machine+'_'+metric
# register an Agent for this Machine
try:
test = MLbureau.member[Name]
except:
MLbureau.member[Name] = swap.Agent_ML(Name, metric)
#---------------------------------------------------------------
# TRAIN THE MACHINE; EVALUATE ON VALIDATION SAMPLE
#---------------------------------------------------------------
# Now we run the machine -- need cross validation on whatever size
# training sample we have ..
# For now this will be fixed until we build in other machine options
params = {'n_neighbors':np.arange(1, 2*(len(train_sample)-1) / 3, 2),
'weights':('uniform','distance')}
# Create the model
general_model = GridSearchCV(estimator=KNC(), param_grid=params,
error_score=0, scoring=metric)
# Train the model -- k-fold cross validation is embedded
trained_model = general_model.fit(train_features, train_labels)
# Test "accuracy" (metric of choice) on validation sample
score = trained_model.score(valid_features, valid_labels)
MLbureau.member[Name].record_training(\
model_described_by=trained_model.best_estimator_,
with_params=trained_model.best_params_,
trained_on=len(train_features),
at_time=TIME,
with_train_acc=traineed_model.best_score_,
and_valid_acc=trained_model.score(valid_features,
valid_labels))
# Store the trained machine
MLbureau.member[Name].model = trained_model
# Compute / store confusion matrix as a function of threshold
# produced by this machine on the Expert Validation sample
fps, tps, thresh = mtrx._binary_clf_curve(valid_labels,
trained_model.predict_proba(valid_features)[:,1])
metric_list = mtrx.compute_binary_metrics(fps, tps)
ACC, TPR, FPR, FNR, TNR, PPV, FDR, FOR, NPV = metric_list
MLbureau.member[Name].record_evaluation(accuracy=ACC,
completeness_s=TPR,
contamination_s=FDR,
completeness_f=TNR,
contamination_f=NPV)
pdb.set_trace()
# 3. compare the metric of choice with the evaluation criterion to
# see if this machine has sufficiently learned?
# ... what if my criterion is simply "Maximize Accuracy"?
# ... or minimize feature contamination? these require that we
# compare tonight's machine with the previous night's machine
# But if my criterion is simply "have feature contam less than 20%"
# then it's easy....
# IF TRAINED MACHINE PREDICTS WELL ON VALIDATION ....
if MLbureau.member[Name].evaluate():
#---------------------------------------------------------------
# APPLY MACHINE TO TEST SAMPLE
#---------------------------------------------------------------
# This requires that my runKNC function returns the Machine Object
shitski=5
#---------------------------------------------------------------
# PROCESS PREDICTIONS/PROBS
#---------------------------------------------------------------
for s,p,l in zip(test_meta, probas, predictions):
ID = str(s['id'])
descriptions = Nair_or_Not(s)
category, kind, flavor, truth = descriptions
# LOAD EACH TEST SUBJECT INTO MACHINE COLLECTION
# -------------------------------------------------------------
try:
test = MLsample.member[ID]
except: MLsample.member[ID] = swap.Subject_ML(ID,
str(s['name']), category, kind,
truth,threshold,s['external_ref'])
tstring = datetime.now().strftime('%Y-%m-%d_%H:%M:%S')
MLsample.member[ID].was_described(by='knn', as_being=1,
withp=p, at_time=tstring)
# NOTE: if subject is Nair (training) it doesn't get flagged as
# inactive but it can be flagged as detected/rejected
# IF MACHINE P >= THRESHOLD, INSERT INTO SWAP COLLECTION
# -------------------------------------------------------------
thresholds = {'detection':0.,'rejection':0.}
if (p >= threshold) or (1-p >= threshold):
print "BOOM! WE'VE GOT A MACHINE-CLASSIFIED SUBJECT:"
print "Probability:",p
# Initialize the subject in SWAP Collection
sample.member[ID] = swap.Subject(ID, str(s['name']),
category, kind,flavor,truth,
thresholds, s['external_ref'],0.)
sample.member[ID].retiredby = 'machine'
# Flag subject as 'INACTIVE' / 'DETECTED' / 'REJECTED'
# ----------------------------------------------------------
if p >= threshold:
sample.member[str(s['id'])].state = 'inactive'
elif 1-p >= threshold:
sample.member[str(s['id'])].status = 'rejected'
#---------------------------------------------------------------
# SAVE MACHINE METADATA?
#---------------------------------------------------------------
print "Size of SWAP sample:", sample.size()
print "Size of ML sample:", MLsample.size()
if tonights.parameters['report']:
# Output list of subjects to retire, based on this batch of
# classifications. Note that what is needed here is the ZooID,
# not the subject ID:
new_retirementfile = swap.get_new_filename(tonights.parameters,\
'retire_these', source='ML')
print "SWAP: saving Machine-retired subject Zooniverse IDs..."
N = swap.write_list(MLsample,new_retirementfile,
item='retired_subject', source='ML')
print "SWAP: "+str(N)+" lines written to "+new_retirementfile
# write catalogs of smooth/not over MLthreshold
# -------------------------------------------------------------
catalog = swap.get_new_filename(tonights.parameters,
'retired_catalog', source='ML')
print "SWAP: saving catalog of Machine-retired subjects..."
Nretired, Nsubjects = swap.write_catalog(MLsample,bureau,
catalog, threshold,
kind='rejected', source='ML')
print "SWAP: From "+str(Nsubjects)+" subjects classified,"
print "SWAP: "+str(Nretired)+" retired (with P < rejection) "\
"written to "+catalog
catalog = swap.get_new_filename(tonights.parameters,
'detected_catalog', source='ML')
print "SWAP: saving catalog of Machine detected subjects..."
Ndetected, Nsubjects = swap.write_catalog(MLsample, bureau,
catalog, threshold,
kind='detected', source='ML')
print "SWAP: From "+str(Nsubjects)+" subjects classified,"
print "SWAP: %i detected (with P > MLthreshold) "\
"written to %s"%(Ndetected, catalog)
# If is hasn't been done already, save the current directory
# ---------------------------------------------------------------------
tonights.parameters['dir'] = os.getcwd()+'/'+tonights.parameters['trunk']
if not os.path.exists(tonights.parameters['dir']):
os.makedirs(tonights.parameters['dir'])
# Repickle all the shits
# -----------------------------------------------------------------------
if tonights.parameters['repickle']:
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "SWAP: saving SWAP subjects to "+new_samplefile
swap.write_pickle(sample,new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
new_samplefile=swap.get_new_filename(tonights.parameters,'MLcollection')
print "SWAP: saving test sample subjects to "+new_samplefile
swap.write_pickle(MLsample,new_samplefile)
tonights.parameters['MLsamplefile'] = new_samplefile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "SWAP: saving metadata to "+metadatafile
swap.write_pickle(subjects,metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# Update the time increment for SWAP's next run
# -----------------------------------------------------------------------
t2 = datetime.datetime.strptime(tonights.parameters['start'],
'%Y-%m-%d_%H:%M:%S') + \
datetime.timedelta(days=tonights.parameters['increment'])
tstop = datetime.datetime.strptime(tonights.parameters['end'],
'%Y-%m-%d_%H:%M:%S')
if t2 == tstop:
plots = True
else:
tonights.parameters['start'] = t2.strftime('%Y-%m-%d_%H:%M:%S')
# Update configfile to reflect Machine additions
# -----------------------------------------------------------------------
configfile = 'update.config'
random_file = open(tonights.parameters['random_file'],"w");
random_state = np.random.get_state();
cPickle.dump(random_state,random_file);
random_file.close();
swap.write_config(configfile, tonights.parameters)
pdb.set_trace()
print "SWAP: "+str(Ndetected)+" detected (with P > acceptance) "\
"written to "+catalog
# ------------------------------------------------------------------
# Pickle the bureau, sample, and database, if required. If we do
# this, its because we want to pick up from where we left off
# (ie with SWAPSHOP) - so save the pickles in the $cwd. This is
# taken care of in io.py. Note that we update the parameters as
# we go - this will be useful later when we write update.config.
if tonights.parameters['repickle'] and count > 0:
new_bureaufile = swap.get_new_filename(tonights.parameters,'bureau')
print "SWAP: saving agents to "+new_bureaufile
swap.write_pickle(bureau,new_bureaufile)
tonights.parameters['bureaufile'] = new_bureaufile
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "SWAP: saving subjects to "+new_samplefile
swap.write_pickle(sample,new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "SWAP: saving metadata to "+metadatafile
swap.write_pickle(subjects,metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# ------------------------------------------------------------------
# If there is more to do we need to update the config file for the next day
# Pickle the bureau, sample, and database, if required. If we do
# this, its because we want to pick up from where we left off
# (ie with SWAPSHOP) - so save the pickles in the $cwd. This is
# taken care of in io.py. Note that we update the parameters as
# we go - this will be useful later when we write update.config.
if tonights.parameters['repickle'] and count > 0:
# 8-4-16: MB just learned that constantly appending numpy
# arrays is vastly more expensive and slow!
# Instead -- make agent and subject histories python lists
# If we want to pickle the object, THEN cast them as numpy arrays
new_bureaufile = swap.get_new_filename(tonights.parameters,'bureau')
print "SWAP: saving agents to "+new_bureaufile
swap.write_pickle(bureau,new_bureaufile)
tonights.parameters['bureaufile'] = new_bureaufile
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "SWAP: saving subjects to "+new_samplefile
swap.write_pickle(sample,new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "SWAP: saving metadata to "+metadatafile
swap.write_pickle(storage,metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# ------------------------------------------------------------------
# If there is more to do we need to update the config file for the next day
def MachineClassifier(options, args):
"""
NAME
MachineClassifier.py
PURPOSE
Machine learning component of Galaxy Zoo Express
Read in a training sample generated by human users (which have
preferentially been analyzed by SWAP).
Learn on the training sample and moniter progress.
Once "fully trained", apply learned model to test sample.
COMMENTS
Lots I'm sure.
FLAGS
-h Print this message
-c config file name
"""
# Check for setup file in array args:
if (len(args) >= 1) or (options.configfile):
if args: config = args[0]
elif options.configfile: config = options.configfile
print swap.doubledashedline
print swap.ML_hello
print swap.doubledashedline
print "ML: taking instructions from",config
else:
print MachineClassifier.__doc__
return
tonights = swap.Configuration(config)
# Read the pickled random state file
random_file = open(tonights.parameters['random_file'],"r");
random_state = cPickle.load(random_file);
random_file.close();
np.random.set_state(random_state);
time = tonights.parameters['start']
print time
# Get the machine threshold (make retirement decisions)
threshold = tonights.parameters['machine_threshold']
prior = tonights.parameters['prior']
# Get list of evaluation metrics and criteria
eval_metrics = tonights.parameters['evaluation_metrics']
# How much cross-validation should we do?
cv = tonights.parameters['cross_validation']
survey = tonights.parameters['survey']
#----------------------------------------------------------------------
# read in the metadata for all subjects (Test or Training sample?)
storage = swap.read_pickle(tonights.parameters['metadatafile'], 'metadata')
subjects = storage.subjects
#----------------------------------------------------------------------
# read in the SWAP collection
sample = swap.read_pickle(tonights.parameters['samplefile'],'collection')
#----------------------------------------------------------------------
# read in or create the ML collection
MLsample = swap.read_pickle(tonights.parameters['MLsamplefile'],
'MLcollection')
# read in or create the ML bureau for machine agents (history)
MLbureau = swap.read_pickle(tonights.parameters['MLbureaufile'],'bureau')
#if not tonights.parameters['MLbureaufile']:
# MLbureaufile = swap.get_new_filename(tonights.parameters,'bureau','ML')
# tonights.parameters['MLbureaufile'] = MLbureaufile
#MLbureau = swap.read_pickle(tonights.parameters['MLbureaufile'],'bureau')
#-----------------------------------------------------------------------
# SELECT TRAINING & VALIDATION SAMPLES
#-----------------------------------------------------------------------
# TO DO: training sample should only select those which are NOT part of
# validation sample (Nair catalog objects) 2/22/16
train_sample = storage.fetch_subsample(sample_type='train',
class_label='GZ2_label')
""" Notes about the training sample:
# this will select only those which have my morphology measured for them
# AND which have a true "answer" according to GZ2
# Eventually we could open this up to include the ~10k that aren't in the
# GZ Main Sample but I think, for now, we should reduce ourselves to this
# stricter sample so that we always have back-up "truth" for each galaxy.
"""
try:
train_meta, train_features = ml.extract_features(train_sample)
original_length = len(train_meta)
except TypeError:
print "ML: can't extract features from subsample."
print "ML: Exiting MachineClassifier.py"
sys.exit()
else:
# TODO: consider making this part of SWAP's duties?
# 5/18/16: Only use those subjects which are no longer on the prior
off_the_fence = np.where(train_meta['SWAP_prob']!=prior)
train_meta = train_meta[off_the_fence]
train_features = train_features[off_the_fence]
train_labels = np.array([1 if p > prior else 0 for p in
train_meta['SWAP_prob']])
#train_labels = train_meta['Nair_label'].filled()
shortened_length = len(train_meta)
print "ML: found a training sample of %i subjects"%shortened_length
removed = original_length - shortened_length
print "ML: %i subjects had prior probability and were removed"%removed
valid_sample = storage.fetch_subsample(sample_type='valid',
class_label='Expert_label')
try:
valid_meta, valid_features = ml.extract_features(valid_sample)
except:
print "ML: there are no subjects with the label 'valid'!"
else:
valid_labels = valid_meta['Expert_label'].filled()
print "ML: found a validation sample of %i subjects"%len(valid_meta)
# ---------------------------------------------------------------------
# Require a minimum size training sample [Be reasonable, my good man!]
# ---------------------------------------------------------------------
if len(train_sample) < 10000:
print "ML: training sample is too small to be worth anything."
print "ML: Exiting MachineClassifier.py"
sys.exit()
else:
print "ML: training sample is large enough to give it a shot."
# TODO: LOOP THROUGH DIFFERENT MACHINES?
# 5/12/16 -- no... need to make THIS a class and create multiple
# instances? Each one can be passed an instance of a machine?
# Machine can be trained to maximize/minimize different metrics
# (ACC, completeness, purity, etc. Have a list of acceptable ones.)
# Minimize a Loss function (KNC doesn't have a loss fcn).
for metric in eval_metrics:
# REGISTER Machine Classifier
# Construct machine name --> Machine+Metric? For now: KNC
machine = 'KNC'
machine = 'RF'
Name = machine+'_'+metric
# register an Agent for this Machine
# This "Agent" doesn't behave like a SW agent... at least not yet
try:
test = MLbureau.member[Name]
except:
MLbureau.member[Name] = swap.Agent_ML(Name, metric)
MLagent = MLbureau.member[Name]
#---------------------------------------------------------------
# TRAIN THE MACHINE; EVALUATE ON VALIDATION SAMPLE
#---------------------------------------------------------------
# Now we run the machine -- need cross validation on whatever size
# training sample we have ..
# Fixed until we build in other machine options
# Need to dynamically determine appropriate parameters...
#max_neighbors = get_max_neighbors(train_features, cv)
#n_neighbors = np.arange(1, (cv-1)*max_neighbors/cv, 5, dtype=int)
#params = {'n_neighbors':n_neighbors,
# 'weights':('uniform','distance')}
num_features = train_features.shape[1]
min_features = int(round(np.sqrt(num_features)))
params = {'max_features':np.arange(min_features, num_features+1),
'max_depth':np.arange(2,16)}
# Create the model
# for "estimator=XXX" all you need is an instance of a machine --
# any scikit-learn machine will do. However, non-sklearn machines..
# That will be a bit trickier! (i.e. Phil's conv-nets)
general_model = GridSearchCV(estimator=RF(n_estimators=30),
param_grid=params, n_jobs=-1,
error_score=0, scoring=metric, cv=cv)
# Train the model -- k-fold cross validation is embedded
print "ML: Searching the hyperparameter space for values that "\
"optimize the %s."%metric
trained_model = general_model.fit(train_features, train_labels)
MLagent.model = trained_model
# Test "accuracy" (metric of choice) on validation sample
score = trained_model.score(valid_features, valid_labels)
ratio = np.sum(train_labels==1) / len(train_labels)
MLagent.record_training(model_described_by=
trained_model.best_estimator_,
with_params=trained_model.best_params_,
trained_on=len(train_features),
with_ratio=ratio,
at_time=time,
with_train_score=trained_model.best_score_,
and_valid_score=trained_model.score(
valid_features, valid_labels))
fps, tps, thresh = mtrx.roc_curve(valid_labels,
trained_model.predict_proba(valid_features)[:,1])
metric_list = compute_binary_metrics(fps, tps)
ACC, TPR, FPR, FNR, TNR, PPV, FDR, FOR, NPV = metric_list
MLagent.record_validation(accuracy=ACC, recall=TPR, precision=PPV,
false_pos=FPR, completeness_f=TNR,
contamination_f=NPV)
#MLagent.plot_ROC()
# ---------------------------------------------------------------
# IF TRAINED MACHINE PREDICTS WELL ON VALIDATION ....
# ---------------------------------------------------------------
if MLagent.is_trained(metric):
print "ML: %s has successfully trained and will be applied "\
"to the test sample."
# Retrieve the test sample
test_sample = storage.fetch_subsample(sample_type='test',
class_label='GZ2_label')
""" Notes on test sample:
The test sample will, in real life, be those subjects for which
we don't have an answer a priori. However, for now, this sample
is how we will judge, in part, the performance of the overall
method. As such, we only include those subjects which have
GZ2 labels in the Main Sample.
"""
try:
test_meta, test_features = ml.extract_features(test_sample)
except:
print "ML: there are no subjects with the label 'test'!"
print "ML: which means there's nothing more to do!"
else:
print "ML: found test sample of %i subjects"%len(test_meta)
#-----------------------------------------------------------
# APPLY MACHINE TO TEST SAMPLE
#-----------------------------------------------------------
predictions = MLagent.model.predict(test_features)
probabilities = MLagent.model.predict_proba(test_features)
print "ML: %s has finished predicting labels for the test "\
"sample."%Name
print "ML: Generating performance report on the test sample:"
test_labels = test_meta['GZ2_label'].filled()
print mtrx.classification_report(test_labels, predictions)
test_accuracy=mtrx.accuracy_score(test_labels,predictions)
test_precision=mtrx.precision_score(test_labels,predictions)
test_recall=mtrx.recall_score(test_labels,predictions)
MLagent.record_evaluation(accuracy_score=test_accuracy,
precision_score=test_precision,
recall_score=test_recall,
at_time=time)
#pdb.set_trace()
# ----------------------------------------------------------
# Save the predictions and probabilities to a new pickle
test_meta['predictions'] = predictions
test_meta['probability_of_smooth'] = probabilities[:,1]
filename=tonights.parameters['trunk']+'_'+Name+'.pickle'
swap.write_pickle(test_meta, filename)
"""
for thing, pred, p in zip(test_meta, predictions,
probabitilies):
# IF MACHINE P >= THRESHOLD, INSERT INTO SWAP COLLECTION
# --------------------------------------------------------
if (p >= threshold) or (1-p >= threshold):
print "BOOM! WE'VE GOT A MACHINE-CLASSIFIED SUBJECT:"
print "Probability:", p
# Initialize the subject in SWAP Collection
ID = thing['asset_id']
sample.member[ID] = swap.Subject(ID, str(s['SDSS_id']),
location=s['external_ref'])
sample.member[ID].retiredby = 'machine'
# Flag subject as 'INACTIVE' / 'DETECTED' / 'REJECTED'
# ----------------------------------------------------------
if p >= threshold:
sample.member[str(s['id'])].state = 'inactive'
elif 1-p >= threshold:
sample.member[str(s['id'])].status = 'rejected'
#"""
# If is hasn't been done already, save the current directory
# ---------------------------------------------------------------------
tonights.parameters['dir'] = os.getcwd()+'/'+tonights.parameters['trunk']
if not os.path.exists(tonights.parameters['dir']):
os.makedirs(tonights.parameters['dir'])
# Repickle all the shits
# -----------------------------------------------------------------------
if tonights.parameters['repickle']:
new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
print "ML: saving SWAP subjects to "+new_samplefile
swap.write_pickle(sample, new_samplefile)
tonights.parameters['samplefile'] = new_samplefile
new_samplefile=swap.get_new_filename(tonights.parameters,'MLcollection')
print "ML: saving test sample subjects to "+new_samplefile
swap.write_pickle(MLsample,new_samplefile)
tonights.parameters['MLsamplefile'] = new_samplefile
new_bureaufile=swap.get_new_filename(tonights.parameters,'bureau','ML')
print "ML: saving MLbureau to "+new_bureaufile
swap.write_pickle(MLbureau, new_bureaufile)
tonights.parameters['MLbureaufile'] = new_bureaufile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "ML: saving metadata to "+metadatafile
swap.write_pickle(storage, metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# UPDATE CONFIG FILE with pickle filenames, dir/trunk, and (maybe) new day
# ----------------------------------------------------------------------
configfile = config.replace('startup','update')
# Random_file needs updating, else we always start from the same random
# state when update.config is reread!
random_file = open(tonights.parameters['random_file'],"w");
random_state = np.random.get_state();
cPickle.dump(random_state,random_file);
random_file.close();
swap.write_config(configfile, tonights.parameters)
return
def MachineClassifier(options, args):
"""
NAME
MachineClassifier.py
PURPOSE
Machine learning component of Galaxy Zoo Express
Read in a training sample generated by human users (which have
previously been analyzed by SWAP).
Learn on the training sample and moniter progress.
Once "fully trained", apply learned model to test sample.
COMMENTS
Lots I'm sure.
FLAGS
-h Print this message
-c config file name
"""
#-----------------------------------------------------------------------
# LOAD CONFIG FILE PARAMETERS
#-----------------------------------------------------------------------
# Check for config file in array args:
if (len(args) >= 1) or (options.configfile):
if args: config = args[0]
elif options.configfile: config = options.configfile
print swap.doubledashedline
print swap.ML_hello
print swap.doubledashedline
print "ML: taking instructions from",config
else:
print MachineClassifier.__doc__
return
machine_sim_directory = 'sims_Machine/redo_with_circular_morphs/'
tonights = swap.Configuration(config)
# Read the pickled random state file
random_file = open(tonights.parameters['random_file'],"r");
random_state = cPickle.load(random_file);
random_file.close();
np.random.set_state(random_state)
time = tonights.parameters['start']
# Get the machine threshold (to make retirement decisions)
swap_thresholds = {}
swap_thresholds['detection'] = tonights.parameters['detection_threshold']
swap_thresholds['rejection'] = tonights.parameters['rejection_threshold']
threshold = tonights.parameters['machine_threshold']
prior = tonights.parameters['prior']
# Get list of evaluation metrics and criteria
eval_metrics = tonights.parameters['evaluation_metrics']
# How much cross-validation should we do?
cv = tonights.parameters['cross_validation']
survey = tonights.parameters['survey']
# To generate training labels based on the subject probability,
# we need to know what should be considered the positive label:
# i.e., GZ2 has labels (in metadatafile) Smooth = 1, Feat = 0
# Doing a Smooth or Not run, the positive label is 1
# Doing a Featured or Not run, the positive label is 0
pos_label = tonights.parameters['positive_label']
#----------------------------------------------------------------------
# read in the metadata for all subjects
storage = swap.read_pickle(tonights.parameters['metadatafile'], 'metadata')
# 11TH HOUR QUICK FIX CUZ I F****D UP. MB 10/27/16
if 'GZ2_raw_combo' not in storage.subjects.colnames:
gz2_metadata = Table.read('metadata_ground_truth_labels.fits')
storage.subjects['GZ2_raw_combo'] = gz2_metadata['GZ2_raw_combo']
swap.write_pickle(storage, tonights.parameters['metadatafile'])
subjects = storage.subjects
#----------------------------------------------------------------------
# read in the PROJECT COLLECTION -- (shared between SWAP/Machine)
#sample = swap.read_pickle(tonights.parameters['samplefile'],'collection')
# read in or create the ML bureau for machine agents (history for Machines)
MLbureau = swap.read_pickle(tonights.parameters['MLbureaufile'],'bureau')
#-----------------------------------------------------------------------
# FETCH TRAINING & VALIDATION SAMPLES
#-----------------------------------------------------------------------
train_sample = storage.fetch_subsample(sample_type='train',
class_label='GZ2_raw_combo')
""" Notes about the training sample:
# this will select only those which have my morphology measured for them
# AND which have "ground truth" according to GZ2
# Eventually we could open this up to include the ~10k that aren't in the
# GZ Main Sample but I think, for now, we should reduce ourselves to this
# stricter sample so that we always have back-up "truth" for each galaxy.
"""
try:
train_meta, train_features = ml.extract_features(train_sample,
keys=['M20_corr', 'C_corr', 'E', 'A_corr', 'G_corr'])
original_length = len(train_meta)
except TypeError:
print "ML: can't extract features from subsample."
print "ML: Exiting MachineClassifier.py"
sys.exit()
else:
# TODO: consider making this part of SWAP's duties?
# 5/18/16: Only use those subjects which are no longer on the prior
off_the_fence = np.where(train_meta['SWAP_prob']!=prior)
train_meta = train_meta[off_the_fence]
train_features = train_features[off_the_fence]
train_labels = np.array([pos_label if p > prior else 1-pos_label
for p in train_meta['SWAP_prob']])
shortened_length = len(train_meta)
print "ML: found a training sample of %i subjects"%shortened_length
removed = original_length - shortened_length
print "ML: %i subjects removed to create balanced training sample"%removed
valid_sample = storage.fetch_subsample(sample_type='valid',
class_label='Expert_label')
try:
valid_meta, valid_features = ml.extract_features(valid_sample,
keys=['M20_corr', 'C_corr', 'E', 'A_corr', 'G_corr'])
except:
print "ML: there are no subjects with the label 'valid'!"
else:
valid_labels = valid_meta['Expert_label'].filled()
print "ML: found a validation sample of %i subjects"%len(valid_meta)
# ---------------------------------------------------------------------
# Require a minimum size training sample [Be reasonable, my good man!]
# ---------------------------------------------------------------------
if len(train_sample) < 10000:
print "ML: training sample is too small to be worth anything."
print "ML: Exiting MachineClassifier.py"
sys.exit()
else:
print "ML: training sample is large enough to give it a shot."
# TODO: LOOP THROUGH DIFFERENT MACHINES?
# 5/12/16 -- no... need to make THIS a class and create multiple
# instances? Each one can be passed an instance of a machine?
# Machine can be trained to optimize different metrics
# (ACC, completeness, purity, etc. Have a list of acceptable ones.)
# Minimize a Loss function.
for metric in eval_metrics:
# REGISTER Machine Classifier
# Construct machine name --> Machine+Metric
machine = 'RF'
Name = machine+'_'+metric
# register an Agent for this Machine
try:
test = MLbureau.member[Name]
except:
MLbureau.member[Name] = swap.Agent_ML(Name, metric)
MLagent = MLbureau.member[Name]
#---------------------------------------------------------------
# TRAIN THE MACHINE; EVALUATE ON VALIDATION SAMPLE
#---------------------------------------------------------------
# Now we run the machine -- need cross validation on whatever size
# training sample we have ..
# Fixed until we build in other machine options
# Need to dynamically determine appropriate parameters...
#max_neighbors = get_max_neighbors(train_features, cv)
#n_neighbors = np.arange(1, (cv-1)*max_neighbors/cv, 5, dtype=int)
#params = {'n_neighbors':n_neighbors,
# 'weights':('uniform','distance')}
num_features = train_features.shape[1]
min_features = int(round(np.sqrt(num_features)))
params = {'max_features':np.arange(min_features, num_features+1),
'max_depth':np.arange(2,16)}
# Create the model
# for "estimator=XXX" all you need is an instance of a machine --
# any scikit-learn machine will do. However, non-sklearn machines..
# That will be a bit trickier! (i.e. Phil's conv-nets)
general_model = GridSearchCV(estimator=RF(n_estimators=30),
param_grid=params, n_jobs=31,
error_score=0, scoring=metric, cv=cv)
# Train the model -- k-fold cross validation is embedded
print "ML: Searching the hyperparameter space for values that "\
"optimize the %s."%metric
trained_model = general_model.fit(train_features, train_labels)
MLagent.model = trained_model
# Test accuracy (metric of choice) on validation sample
score = trained_model.score(valid_features, valid_labels)
ratio = np.sum(train_labels==pos_label) / len(train_labels)
MLagent.record_training(model_described_by=
trained_model.best_estimator_,
with_params=trained_model.best_params_,
trained_on=len(train_features),
with_ratio=ratio,
at_time=time,
with_train_score=trained_model.best_score_,
and_valid_score=trained_model.score(
valid_features, valid_labels))
valid_prob_thresh = trained_model.predict_proba(valid_features)[:,pos_label]
fps, tps, thresh = mtrx.roc_curve(valid_labels,valid_prob_thresh, pos_label=pos_label)
metric_list = compute_binary_metrics(fps, tps)
ACC, TPR, FPR, FNR, TNR, PPV, FDR, FOR, NPV = metric_list
MLagent.record_validation(accuracy=ACC, recall=TPR, precision=PPV,
false_pos=FPR, completeness_f=TNR,
contamination_f=NPV)
#MLagent.plot_ROC()
# ---------------------------------------------------------------
# IF TRAINED MACHINE PREDICTS WELL ON VALIDATION ....
# ---------------------------------------------------------------
if MLagent.is_trained(metric) or MLagent.trained:
print "ML: %s has successfully trained and will be applied "\
"to the test sample."%Name
# Retrieve the test sample
test_sample = storage.fetch_subsample(sample_type='test',
class_label='GZ2_raw_combo')
""" Notes on test sample:
The test sample will, in real life, be those subjects for which
we don't have an answer a priori. However, for now, this sample
is how we will judge, in part, the performance of the overall
method. As such, we only include those subjects which have
GZ2 labels in the Main Sample.
"""
try:
test_meta, test_features = ml.extract_features(test_sample,
keys=['M20_corr', 'C_corr', 'E', 'A_corr', 'G_corr'])
except:
print "ML: there are no subjects with the label 'test'!"
print "ML: Either there is nothing more to do or there is a BIG mistake..."
else:
print "ML: found test sample of %i subjects"%len(test_meta)
#-----------------------------------------------------------
# APPLY MACHINE TO TEST SAMPLE
#-----------------------------------------------------------
predictions = MLagent.model.predict(test_features)
probabilities = MLagent.model.predict_proba(test_features)[:,pos_label]
print "ML: %s has finished predicting labels for the test "\
"sample."%Name
print "ML: Generating performance report on the test sample:"
test_labels = test_meta['GZ2_raw_combo'].filled()
print mtrx.classification_report(test_labels, predictions)
test_accuracy = mtrx.accuracy_score(test_labels,predictions)
test_precision = mtrx.precision_score(test_labels,predictions,pos_label=pos_label)
test_recall = mtrx.recall_score(test_labels,predictions,pos_label=pos_label)
MLagent.record_evaluation(accuracy_score=test_accuracy,
precision_score=test_precision,
recall_score=test_recall,
at_time=time)
# ----------------------------------------------------------
# Save the predictions and probabilities to a new pickle
test_meta['predictions'] = predictions
test_meta['machine_probability'] = probabilities
# If is hasn't been done already, save the current directory
# ---------------------------------------------------------------------
tonights.parameters['trunk'] = survey+'_'+tonights.parameters['start']
# This is the standard directory...
#tonights.parameters['dir'] = os.getcwd()+'/'+tonights.parameters['trunk']
# This is to put files into the sims_Machine/... directory.
tonights.parameters['dir'] = os.getcwd()
filename=tonights.parameters['dir']+'/'+tonights.parameters['trunk']+'_'+Name+'.fits'
test_meta.write(filename)
count=0
noSWAP=0
for sub, pred, prob in zip(test_meta, predictions, probabilities):
# IF MACHINE P >= THRESHOLD, INSERT INTO SWAP COLLECTION
# --------------------------------------------------------
if (prob >= threshold) or (1-prob >= threshold):
# Flip the set label in the metadata file --
# don't want to use this as a training sample!
idx = np.where(subjects['asset_id'] == sub['asset_id'])
storage.subjects['MLsample'][idx] = 'mclass'
storage.subjects['retired_date'][idx] = time
count+=1
print "MC: Machine classifed {0} subjects with >= 90% confidence".format(count)
print "ML: Of those, {0} had never been seen by SWAP".format(noSWAP)
tonights.parameters['trunk'] = survey+'_'+tonights.parameters['start']
tonights.parameters['dir'] = os.getcwd()
if not os.path.exists(tonights.parameters['dir']):
os.makedirs(tonights.parameters['dir'])
# Repickle all the shits
# -----------------------------------------------------------------------
if tonights.parameters['repickle']:
#new_samplefile = swap.get_new_filename(tonights.parameters,'collection')
#print "ML: saving SWAP subjects to "+new_samplefile
#swap.write_pickle(sample, new_samplefile)
#tonights.parameters['samplefile'] = new_samplefile
new_bureaufile=swap.get_new_filename(tonights.parameters,'bureau','ML')
print "ML: saving MLbureau to "+new_bureaufile
swap.write_pickle(MLbureau, new_bureaufile)
tonights.parameters['MLbureaufile'] = new_bureaufile
metadatafile = swap.get_new_filename(tonights.parameters,'metadata')
print "ML: saving metadata to "+metadatafile
swap.write_pickle(storage, metadatafile)
tonights.parameters['metadatafile'] = metadatafile
# UPDATE CONFIG FILE with pickle filenames, dir/trunk, and (maybe) new day
# ----------------------------------------------------------------------
configfile = config.replace('startup','update')
# Random_file needs updating, else we always start from the same random
# state when update.config is reread!
random_file = open(tonights.parameters['random_file'],"w");
random_state = np.random.get_state();
cPickle.dump(random_state,random_file);
random_file.close();
swap.write_config(configfile, tonights.parameters)
return
def make_lens_catalog(args):
"""
NAME
make_lens_catalog
PURPOSE
Given location of collection pickle, this script produces a set of
annotated images of lenses (heatmaps for lens locations, markers for
where clicks were, etc).
COMMENTS
You have to download the file so it chooses whever your output
directory is to also download the raw images.
This should be pretty customizable.
FLAGS
-h Print this message
--skill Weight by skill
INPUTS
collection.pickle
OUTPUTS
lens.dat
Assumed format:
ID kind x y Prob N0 Skill Dist
Here:
ID = Space Warps subject ID
kind = Space Warps subject type (sim, dud, test)
x,y = object (cluster) centroid, in pixels
P = Space Warps subject probability
N0 = number of markers in the cluster
S = total skill per cluster, summed over markers
D = biggest distance within cluster
EXAMPLE
BUGS
AUTHORS
This file is part of the Space Warps project, and is distributed
under the GPL v2 by the Space Warps Science Team.
http://spacewarps.org/
HISTORY
2013-07-16 started Davis (KIPAC)
"""
# ------------------------------------------------------------------
# Some defaults:
flags = {
'skill': False,
'output_directory': './',
'output_name': 'catalog.dat',
'image_y_size': 440,
'catalog_path': '',
'update_collection': '',
}
# ------------------------------------------------------------------
# Read in options:
# this has to be easier to do...
for arg in args:
if arg in flags:
flags[arg] = args[arg]
elif arg == 'collection_path':
collection_path = args[arg]
else:
print "make_lens_atlas: unrecognized flag ", arg
print "make_lens_catalog: illustrating behaviour captured in collection file: "
print "make_lens_catalog: ", collection_path
memory = joblib.Memory(cachedir=flags['output_directory'])
memory.clear()
catalog_path = flags['output_directory'] + flags['output_name']
if len(flags['output_name']) > 0:
F = open(catalog_path, 'w')
F.write('id,kind,x,y,prob,n0,skill,dist\n')
# ------------------------------------------------------------------
# Read in files:
collection = swap.read_pickle(collection_path, 'collection')
ID_list = collection.list()
print "make_lens_catalog: collection numbers ", len(ID_list)
if flags['catalog_path'] != '':
print "make_lens_catalog: filtering from catalog ", flags[
'catalog_path']
catalog_in = csv2rec(flags['catalog_path'])
ID_list = np.unique(catalog_in['id'])
# ------------------------------------------------------------------
# Run through data:
catalog = {}
for ID in ID_list:
subject = collection.member[ID]
kind = subject.kind
P = subject.mean_probability
itwas = subject.annotationhistory['ItWas']
x_all = subject.annotationhistory['At_X']
y_all = subject.annotationhistory['At_Y']
x_markers = np.array([xi for xj in x_all for xi in xj])
y_markers = np.array([yi for yj in y_all for yi in yj])
catalog.update(
{ID: {
'agents_reject': [],
'x': x_markers,
'y': y_markers,
}})
PL_all = subject.annotationhistory['PL']
PD_all = subject.annotationhistory['PD']
# filter out the empty clicks
PL_list = []
PL_nots = []
for i, xj in enumerate(x_all):
# len(xj) of empty = 0
PL_list.append([PL_all[i]] * len(xj))
if len(xj) == 0:
PL_nots.append(PL_all[i])
PL = np.array([PLi for PLj in PL_list for PLi in PLj])
PL_nots = np.array(PL_nots)
# filter out the empty clicks
PD_list = []
PD_nots = []
for i, xj in enumerate(x_all):
PD_list.append([PD_all[i]] * len(xj))
if len(xj) == 0:
PD_nots.append(PD_all[i])
catalog[ID]['agents_reject'].append(i)
PD = np.array([PDi for PDj in PD_list for PDi in PDj])
PD_nots = np.array(PD_nots)
skill = swap.expectedInformationGain(0.5, PL, PD) # skill
# it is only fair to write out the NOTs, too
# do the empty guys
skill_nots = swap.expectedInformationGain(0.5, PL_nots,
PD_nots) # skill
x, y = -1, -1
N0 = len(skill_nots)
S = np.sum(skill_nots)
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
if len(catalog) % 500 == 0:
print len(catalog)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
if len(x_markers) == 0:
# apparently everyone was a not...
catalog[ID]['agents_labels'] = np.array([])
continue
# ------------------------------------------------------------------
# cluster
print 'make_lens_catalog: subject ID = ', ID
if flags['skill']:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, skill, memory=memory)
else:
cluster_centers, cluster_center_labels, cluster_labels, \
n_clusters, dist_within = outlier_clusters(x_markers, y_markers, None, memory=memory)
# need to get: x, y, N0, S
catalog[ID]['agents_labels'] = cluster_labels
for cluster_center_label in cluster_center_labels:
cluster_center = cluster_centers[cluster_center_label]
members = (cluster_labels == cluster_center_label)
x, y = cluster_center
# convert y to catalog convention
y = flags['image_y_size'] - y
N0 = np.sum(members)
S = np.sum(skill[members])
D = dist_within[cluster_center_label]
if cluster_center_label == -1:
# outlier cluster
# so really every point is its own cluster...
D = 0
## catalog.append((ID, kind, x, y, P, N0, S, D))
## if len(catalog)%500 == 0:
## print len(catalog)
# TODO: make some requirement to be included (exclude outliers)
if len(flags['output_name']) > 0:
F.write('{0},{1},{2},{3},{4},{5},{6},{7}\n'.format(
ID, kind, x, y, P, N0, S, D))
print 'make_lens_catalog: Clearing memory'
# clear memory
memory.clear()
if len(flags['output_name']) > 0:
print 'make_lens_catalog: closing file!'
F.close()
if len(flags['update_collection']) > 0:
print 'make_lens_catalog: writing updated collection to', flags[
'update_collection']
# TODO: get the other params correct!!!!
collection_fat = swap.collection.Collection()
for ID in catalog:
subject = collection.member[ID]
atx = subject.annotationhistory['At_X']
labels_in = list(catalog[ID]['agents_labels'])
labels_fat = []
for atx_i in atx:
labels_fat.append([])
for atx_ij in atx_i:
labels_fat[-1].append(labels_in.pop(0))
subject.annotationhistory.update({'labels': labels_fat})
collection_fat.member.update({ID: subject})
swap.write_pickle(collection_fat, flags['update_collection'])
print 'make_lens_catalog: All done!'
return catalog
